N - mixture models by species
modelling N by site to get relative abundance
abundance by site will be used as a cov on predator occupancy
7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ
Species: Â Â Â Â YellowBelliedMarmot
Detections by Year:
|
Yr
|
2016
|
2017
|
2018
|
2019
|
2020
|
|
sites
|
19
|
31
|
19
|
32
|
26
|
|
detections
|
13
|
63
|
17
|
50
|
24
|
|
N.dot.model
|
4
|
15
|
10
|
54
|
41
|
WAIC
Models by WAIC:
|
model
|
description
|
WAIC
|
N.total.est
|
|
fm7
|
counts
|
13.78466
|
127
|
|
fm4
|
lure + jdt
|
825.63785
|
144
|
|
fm6
|
lure + jdt + jdtSq
|
830.08352
|
144
|
|
fm2
|
jdt
|
841.75801
|
99
|
|
fm5
|
jdt + jdtSq
|
846.14263
|
101
|
|
fm1
|
dot
|
1096.23128
|
124
|
|
fm3
|
lure
|
1117.58635
|
106
|
Model summaries:
model: fm1
summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
p[1]
|
NA
|
8149
|
0.151
|
0.15
|
0.08
|
0.22
|
0
|
1.001
|
|
p[2]
|
NA
|
7043
|
0.163
|
0.159
|
0.12
|
0.20
|
0
|
1.001
|
|
p[3]
|
NA
|
3588
|
0.034
|
0.031
|
0.01
|
0.06
|
0
|
1.0009
|
|
p[4]
|
NA
|
1347
|
0.033
|
0.031
|
0.01
|
0.05
|
0
|
1.0009
|
|
p[5]
|
NA
|
704
|
0.021
|
0.015
|
0.00
|
0.04
|
0
|
0.9981
|
|
lambda[1]
|
NA
|
9289
|
0.238
|
0.191
|
0.06
|
0.41
|
0
|
1.0007
|
|
lambda[2]
|
NA
|
9517
|
0.545
|
0.5
|
0.29
|
0.78
|
0
|
1.001
|
|
lambda[3]
|
NA
|
1875
|
0.905
|
0.714
|
0.30
|
1.46
|
0
|
1.001
|
|
lambda[4]
|
NA
|
441
|
2.042
|
1.458
|
0.80
|
3.15
|
0
|
1.0009
|
|
lambda[5]
|
NA
|
219
|
2.313
|
0.993
|
0.37
|
4.44
|
0
|
1.0011
|
|
N[93]
|
NA
|
1262
|
2.206
|
1
|
1.00
|
4.00
|
0
|
1.0006
|
|
N[67]
|
NA
|
3061
|
3.320
|
2.994
|
2.00
|
5.00
|
0
|
1.001
|
|
N[94]
|
NA
|
1186
|
2.931
|
2.002
|
1.00
|
5.00
|
0
|
1
|
|
N[6]
|
NA
|
9301
|
0.016
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[7]
|
NA
|
9323
|
0.019
|
err
|
0.00
|
0.00
|
err
|
err
|
p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[93]

N[67]

N[94]

N[6]

N[7]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
jdt
|
1729
|
2.131
|
2.127
|
1.84
|
2.43
|
0
|
1.001
|
|
alpha0
|
NA
|
1555
|
-4.439
|
-4.426
|
-4.84
|
-4.00
|
0
|
1.001
|
|
lambda[1]
|
NA
|
6993
|
0.438
|
0.326
|
0.12
|
0.74
|
0
|
1.0008
|
|
lambda[2]
|
NA
|
6067
|
1.226
|
1.119
|
0.68
|
1.77
|
0
|
1.001
|
|
lambda[3]
|
NA
|
5764
|
0.941
|
0.775
|
0.41
|
1.41
|
0
|
1.001
|
|
lambda[4]
|
NA
|
8725
|
0.968
|
0.899
|
0.62
|
1.31
|
0
|
1.001
|
|
lambda[5]
|
NA
|
6517
|
1.042
|
1.014
|
0.57
|
1.54
|
0
|
1.001
|
|
N[70]
|
NA
|
10000
|
0.940
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[115]
|
NA
|
9429
|
1.375
|
1
|
1.00
|
2.00
|
0
|
1
|
|
N[25]
|
NA
|
8888
|
0.159
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[91]
|
NA
|
8260
|
1.308
|
1
|
1.00
|
2.00
|
0
|
1
|
|
N[55]
|
NA
|
9635
|
0.307
|
0
|
0.00
|
1.00
|
1
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[70]

N[115]

N[25]

N[91]

N[55]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
lure
|
7925
|
0.111
|
0.108
|
-0.03
|
0.25
|
0.45582
|
0.8975
|
|
alpha0
|
NA
|
2938
|
-2.947
|
-2.897
|
-3.19
|
-2.66
|
0
|
1.001
|
|
lambda[1]
|
NA
|
6706
|
0.491
|
0.346
|
0.13
|
0.83
|
0
|
1.0008
|
|
lambda[2]
|
NA
|
4063
|
1.618
|
1.415
|
0.92
|
2.31
|
0
|
1.001
|
|
lambda[3]
|
NA
|
8753
|
0.626
|
0.575
|
0.28
|
0.94
|
0
|
1.001
|
|
lambda[4]
|
NA
|
4719
|
1.245
|
1.143
|
0.77
|
1.70
|
0
|
1.001
|
|
lambda[5]
|
NA
|
7793
|
0.672
|
0.625
|
0.35
|
0.98
|
0
|
1.001
|
|
N[76]
|
NA
|
8238
|
2.143
|
1.999
|
1.00
|
3.00
|
0
|
1.0006
|
|
N[47]
|
NA
|
7902
|
2.167
|
1
|
1.00
|
3.00
|
0
|
1.0006
|
|
N[94]
|
NA
|
8644
|
1.954
|
2.003
|
1.00
|
3.00
|
0
|
1.0005
|
|
N[65]
|
NA
|
9433
|
1.323
|
1
|
1.00
|
2.00
|
0
|
1
|
|
N[41]
|
NA
|
7868
|
0.271
|
err
|
0.00
|
1.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[76]

N[47]

N[94]

N[65]

N[41]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
1747
|
-0.649
|
-0.659
|
-0.86
|
-0.42
|
0
|
1.001
|
|
alpha[2]
|
julianDt
|
1008
|
2.513
|
2.503
|
2.18
|
2.87
|
0
|
1.001
|
|
alpha0
|
NA
|
964
|
-4.769
|
-4.728
|
-5.24
|
-4.27
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9701
|
0.321
|
0.228
|
0.09
|
0.55
|
0
|
1.0008
|
|
lambda[2]
|
NA
|
8080
|
0.917
|
0.842
|
0.50
|
1.32
|
0
|
1.001
|
|
lambda[3]
|
NA
|
7673
|
0.797
|
0.71
|
0.36
|
1.19
|
0
|
1.001
|
|
lambda[4]
|
NA
|
8268
|
1.018
|
0.958
|
0.64
|
1.37
|
0
|
1.001
|
|
lambda[5]
|
NA
|
1453
|
3.206
|
2.439
|
1.23
|
5.14
|
0
|
1.001
|
|
N[62]
|
NA
|
7131
|
1.192
|
err
|
1.00
|
2.00
|
err
|
err
|
|
N[31]
|
NA
|
9461
|
0.014
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[11]
|
NA
|
10000
|
0.054
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[70]
|
NA
|
10000
|
1.012
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[61]
|
NA
|
9658
|
0.183
|
err
|
0.00
|
1.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[62]

N[31]

N[11]

N[70]

N[61]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
julianDt
|
141
|
2.997
|
2.84
|
1.97
|
4.16
|
0
|
1.001
|
|
alpha[2]
|
julianDtSq
|
156
|
-0.435
|
-0.406
|
-0.96
|
0.10
|
0.42233
|
0.9072
|
|
alpha0
|
NA
|
158
|
-4.869
|
-4.766
|
-5.51
|
-4.14
|
0
|
1.001
|
|
lambda[1]
|
NA
|
8056
|
0.423
|
0.312
|
0.11
|
0.71
|
0
|
1.0008
|
|
lambda[2]
|
NA
|
5761
|
1.243
|
1.117
|
0.68
|
1.77
|
0
|
1.001
|
|
lambda[3]
|
NA
|
6722
|
0.915
|
0.776
|
0.40
|
1.37
|
0
|
1.001
|
|
lambda[4]
|
NA
|
8269
|
0.981
|
0.933
|
0.62
|
1.32
|
0
|
1.001
|
|
lambda[5]
|
NA
|
5687
|
1.016
|
0.951
|
0.53
|
1.47
|
0
|
1.001
|
|
N[51]
|
NA
|
8846
|
0.546
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[74]
|
NA
|
8743
|
0.063
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[5]
|
NA
|
8542
|
1.923
|
2.002
|
1.00
|
3.00
|
0
|
1.0005
|
|
N[122]
|
NA
|
7869
|
2.015
|
1
|
1.00
|
3.00
|
0
|
1.0005
|
|
N[113]
|
NA
|
9708
|
0.353
|
0
|
0.00
|
1.00
|
1
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[51]

N[74]

N[5]

N[122]

N[113]

julian date relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
1843
|
-0.647
|
-0.607
|
-0.86
|
-0.41
|
0
|
1.001
|
|
alpha[2]
|
julianDt
|
215
|
2.668
|
2.522
|
1.77
|
3.58
|
0
|
1.001
|
|
alpha[3]
|
julianDtSq
|
296
|
-0.075
|
-0.045
|
-0.55
|
0.36
|
0.97918
|
0.5954
|
|
alpha0
|
NA
|
372
|
-4.852
|
-4.756
|
-5.48
|
-4.24
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9067
|
0.319
|
0.228
|
0.09
|
0.55
|
0
|
1.0007
|
|
lambda[2]
|
NA
|
7735
|
0.911
|
0.858
|
0.49
|
1.30
|
0
|
1.001
|
|
lambda[3]
|
NA
|
7503
|
0.798
|
0.707
|
0.37
|
1.22
|
0
|
1.001
|
|
lambda[4]
|
NA
|
7153
|
1.022
|
0.948
|
0.65
|
1.39
|
0
|
1.001
|
|
lambda[5]
|
NA
|
1409
|
3.209
|
2.263
|
1.24
|
5.20
|
0
|
1.001
|
|
N[44]
|
NA
|
10000
|
0.908
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[29]
|
NA
|
8185
|
0.896
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[34]
|
NA
|
10000
|
0.075
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[20]
|
NA
|
10000
|
0.890
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[78]
|
NA
|
10000
|
0.997
|
0
|
0.00
|
2.00
|
1
|
err
|
alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[44]

N[29]

N[34]

N[20]

N[78]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
counts
|
7181
|
13.500
|
13
|
11.46
|
15.50
|
0
|
1.001
|
|
alpha0
|
NA
|
8457
|
-5.884
|
-5.739
|
-6.89
|
-4.88
|
0
|
1.001
|
|
lambda[1]
|
NA
|
7007
|
0.931
|
0.642
|
0.22
|
1.56
|
0
|
1.0008
|
|
lambda[2]
|
NA
|
9303
|
0.977
|
0.872
|
0.51
|
1.39
|
0
|
1.001
|
|
lambda[3]
|
NA
|
10000
|
0.975
|
0.872
|
0.41
|
1.46
|
0
|
1.001
|
|
lambda[4]
|
NA
|
10000
|
0.998
|
0.944
|
0.65
|
1.34
|
0
|
1.001
|
|
lambda[5]
|
NA
|
9483
|
0.982
|
0.928
|
0.51
|
1.39
|
0
|
1.001
|
|
N[37]
|
NA
|
9578
|
0.970
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[53]
|
NA
|
0
|
1.000
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[94]
|
NA
|
0
|
1.000
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[88]
|
NA
|
10000
|
0.974
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[50]
|
NA
|
0
|
1.000
|
err
|
1.00
|
1.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[37]

N[53]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[94]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[88]

N[50]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

alpha relationship
